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bioRxiv · 10.1101/2025.07.20.665785

An NLP-inherited motif confers broad DNA-binding specificity to NIN in root nodule symbiosis

Nosaki, S.·Noda, M.·Onoda, H.·Ito, M.·Suzaki, T.
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Abstract

Nitrogen-fixing root nodule symbiosis (RNS) occurs in some eudicots, including legumes, and is regulated by the transcription factor NODULE INCEPTION (NIN), derived from the NIN-LIKE PROTEIN (NLP) family. However, how the NIN protein acquired RNS-specific functions remains unclear. We identify a previously undescribed motif in Lotus japonicus NIN, located downstream of the RWP-RK domain, which we term the FR. This motif broadens the DNA-binding specificity of NIN by stabilizing the RWP-RK dimer interface. nin mutants lacking the FR motif show defective nodulation and impaired nitrogen fixation. Arabidopsis NLP2 carries a NIN-type FR and shares key features with NIN. Furthermore, the NIN-type FR likely originated as early as gymnosperms, suggesting that the molecular feature of NIN for RNS regulation was inherited from ancestral NLPs before RNS emerged.

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Nosaki, S., Noda, M., Onoda, H., Ito, M., Suzaki, T.. 2025-07-23. An NLP-inherited motif confers broad DNA-binding specificity to NIN in root nodule symbiosis. https://doi.org/10.1101/2025.07.20.665785

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